Skinner's old college friend, Wayne Federman, is making a movie about the bureau and Skinner has given him access to Mulder and Scully during his research phase. Meanwhile, they are attempting to solve a case involving the attempted murder of a Cardinal O'Fallon in the church with Federman interrupting them. In the catacombs of the church, Mulder finds the remains of Micah Hoffman, a 1960's counter-culturalist who disappeared. They search Hoffman's apartment and find many bombs and counterfeiting tools as well as forged gospel of Mary Magdalan. In the basement, they find more remains and pieces of the gospel. Federman wanders off and finds remains that begin moving. He gets freaked and leaves.

Cardinal O'Fallon admits he bought the forged gospel from Hoffman, but believed that it was real. The Lazarus Bowl found at the scene is found to have properties never seen before. During the autopsy of Hoffman, the man comes back to life on the operating table, but when Scully looks down he is back on the operating table. She finishes the autopsy and finds strychnine in his system. Later at church Scully sees a vision of Hoffman again hanging on the cross in the place of Jesus. Mulder arrests Cardinal O'Fallon and Micah Hoffman walks in. Skinner suspends Scully and Mulder for four weeks because of the mix-up, but the Lazarus Bowl actually makes a noise in Aramaic that is one man commanding another to rise from the dead. Hoffman tells Mulder and Scully that he is actually the reincarnation of Jesus Christ and he bombed the church to get rid of the "blasphemous" forgeries.

16 months later, after the film is made, Cardinal O'Fallon kills Micah Hoffman and kills himself. The episode ends

The Dead rise and dance on the graveyard set.

with dead people coming to life on the movie set and Mulder and Scully holding hands on their way presumably to dinner with the FBI credit card Skinner gave them after watching the movie, hinting at the continued romantic relationship between Mulder and Scully that has been hinted at in the last few episodes.

SKINNER: Agent Mulder, Mr. Federman will accompany you today to Christ's Church where he will act as an observer on this case. You will extend to him every courtesy and protection you would a friend of mine and a friend of the Bureau's. Agent Scully, I require your services here for the morning.

MULDER: Sir, have I pissed you off in a way that's more than normal?

SKINNER: Listen, I just wanted to apologize for coming down so hard on you during the Hoffman slash O'Fallon case.

MULDER: Oh. I appreciate that, Skinman.

SKINNER: Don't call me that.

MULDER: Yes, sir.

MULDER (In a bubble bath): Uh... So what are you up to right now, sir?

SKINNER: I'm taking a bubble bath.

MULDER: Uh, hold on just one second, sir. Hey, Scully, Skinman is calling me from a bubble bath.

SKINNER: It's still me, Mulder.

MULDER: Uh, sir, well, hold on one second, sir.

MULDER: Scully?

SCULLY (Also in a bubble bath): Yeah.

MULDER: Yeah, Skinner is calling me from a bubble bath.

SCULLY: Wow, he's really gone Hollywood.

MULDER: Totally.

SCULLY: You know, Mulder, speaking of Hollywood, I think that Tea Leoni has a little crush on you.

MULDER: Oh, yeah, right. Like Tea Leoni's ever going to have a crush on me.

The Zodiac Killer is referenced in this episode as graffiti on a wall that Mulder passes. The symbol can be seen clearly as a circle with two perpendicular lines that cross in the center of said circle.